The -ology part is Greek (linking vowel -ο- plus the stem of λόγος [discourse, reason] plus abstract-noun suffix -ία anglicized to -y); so one approach is to draw upon the Greek word epistēmē (ἐπιστήμη, knowledge, from ἐπίσταμαι, I know) rather than the Latin scientia (knowledge, from sciō, I know), and thus to come up with the word epistemology. Using the Latin abstract noun as given here, what results is scientology. Perhaps unfortunately for your purpose, both forms have come into established usage with specific meanings: epistemology is that branch of philosophy which inquires just what it means to say we know, while Scientology is, ahem, a controversial minority belief system and community founded by L. Ron Hubbard.
The general rule for forming such compounds from classical roots is just to know what the classical roots are, and the specific consonants and vowels that were characteristically used in the classical languages to mediate between these roots and any affixes. This may involve going beyond the mere dictionary form of a classical word. For instance, lyō/λύω is the dictionary form or lemma of a verb meaning either “I set free” or “I destroy” (in Greek and Latin dictionaries, verbs are entered under their first-person singular present indicative active forms); but the many English words derived from it pretty much all use the stem -lys-/-λυσ- from the past or aorist tense elysa/ἔλυσα: paralysis, electrolysis, catalyst, even Lysol. (But then, the s becomes t when the adjectival suffix -ic enters the picture: catalytic, paralytic, etc.)